Homology modeling and phylogenetic relationships of catalases of an opportunistic pathogen Rhizopus oryzae

Linka, Beáta; Szakonyi, Gerda; Petkovits, Tamás; Nagy, László G.; Papp, Tamás; Vágvölgyi, Csaba; Benyhe, Sándor; Ötvös, Ferenc

doi:10.1016/j.lfs.2012.06.016

Cited by 3 publications

(2 citation statements)

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“…Analyses of the phylogeny of the catalase gene has indicated the existence of three primary clades that separated themselves early in the evolution of this gene family by at least two gene duplication events [ 12 ]. A phylogenetic approach could help us account for the intrinsic divergence in enzyme dynamics induced by the natural evolution of sequence variation across time [ 13 ]. As genomics advances, computational tools are becoming increasingly crucial in helping to find and describe possible gene families for various industrial uses.…”

Section: Introductionmentioning

confidence: 99%

Plant catalase in silico characterization and phylogenetic analysis with structural modeling

Takio

Yadav

2022

Journal of Genetic Engineering and Biotechnology

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Background Catalase (EC 1.11.1.6) is a heme-containing tetrameric enzyme that plays a critical role in signaling and hydrogen peroxide metabolism. It was the first enzyme to be crystallized and isolated. Catalase is a well-known industrial enzyme used in diagnostic and analytical methods in the form of biomarkers and biosensors, as well as in the textile, paper, food, and pharmaceutical industries. In silico analysis of CAT genes and proteins has gained increased interest, emphasizing the development of biomarkers and drug designs. The present work aims to understand the catalase evolutionary relationship of plant species and analyze its physicochemical characteristics, homology, phylogenetic tree construction, secondary structure prediction, and 3D modeling of protein sequences and its validation using a variety of conventional computational methods to assist researchers in better understanding the structure of proteins. Results Around 65 plant catalase sequences were computationally evaluated and subjected to bioinformatics assessment for physicochemical characterization, multiple sequence alignment, phylogenetic construction, motif and domain identification, and secondary and tertiary structure prediction. The phylogenetic tree revealed six unique clusters where diversity of plant catalases was found to be the largest for Oryza sativa. The thermostability and hydrophilic nature of these proteins were primarily observed, as evidenced by a relatively high aliphatic index and negative GRAVY value. The distribution of 5 sequence motifs was uniformly distributed with a width length of 50 with the best possible amino residue sequences that resemble the plant catalase PLN02609 superfamily. Using SOPMA, the predicted secondary structure of the protein sequences revealed the predominance of the random coil. The predicted 3D CAT model from Arabidopsis thaliana was a homotetramer, thermostable protein with 59-KDa weight, and its structural validation was confirmed by PROCHECK, ERRAT, Verify3D, and Ramachandran plot. The functional relationships of our query sequence revealed the glutathione reductase as the closest interacting protein of query protein. Conclusions This theoretical plant catalases in silico analysis provide insight into its physiochemical characteristics and functional and structural understanding and its evolutionary behavior and exploring protein structure-function relationships when crystal structures are unavailable.

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Section: Introductionmentioning

confidence: 99%

Plant catalase in silico characterization and phylogenetic analysis with structural modeling

Takio

Yadav

2022

Journal of Genetic Engineering and Biotechnology

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“…Analyses of the catalase genes phylogeny have indicated the existence of three primary clades that separated themselves early in the evolution of this gene family by at least two gene duplication events [16]. The expression of multiple catalase genes in plants is temporally and geographically regulated and is modulated in response to developmental and environmental oxidative stimuli.…”

Section: Introductionmentioning

confidence: 99%

In Silico Studies on Catalases From Plant Sources

Takio

Yadav

2022

Preprint

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Introduction In the era of genomics, bioinformatics has become highly significant, assisting in the genome-wide discovery and characterization of potential genomic regions of different enzymes for a variety of industrial applications. Catalases are unique among environmental biocatalysts due to their high catalytic rate and thermostability. Therefore, present communication deals with the bioinformatics analysis on the characterization of the protein sequence of catalases from diverse plant sources and subjected to assessment of homology, multiple sequence alignment, construction of the phylogenetic tree, amino acid composition, physiochemical properties, motif search, secondary and tertiary structure prediction and its Ramachandran plot . Method In the present study, a total of 65 protein sequences of catalases from diverse plant sources were retrieved from the NCBI database and subjected to bioinformatics assessment for homology search, multiple sequence alignment, phylogenetic tree construction, motif search, and prediction of structural analysis using different in silico analytical tools available. Result The protein sequence of many enzymes have been assessed and analyzed using bioinformatics tools. The diversity of plant sources for catalases was found to be largest for Oryza sativa.The amino acid residue variability in the 65 catalase protein sequences studied ranged from 90 to 533. The molecular weights varied between 10322.46 to 61366.87 daltons, while the pI values varied between 4.53 to 7.95. Thermostability and hydrophilicity were identified in abundance in these proteins, as shown by their relatively high aliphatic index and negative GRAVY values, respectively. The phylogenetic tree displayed unique clusters for each plant genus, and numerous accessions of the same genus were clustered together, suggesting similarity at the sequence level.The prediction of the secondary structure of the catalase showed the predominance of random coil followed by the alpha helix. Ramachandran plot showed that most of the amino acid residues is in the core region which represent the favourable/allowed combination of phi-psi values. The dark region with maximum residues, correspond to no steric hinderance, ie these are the allowed regions for α- helical and β-sheet conformations. Conclusion Five motifs were consistently identified across all sequences, indicating that they were related to the plant catalase PLN02609 family. Plant catalase PLN02609 is found in three kingdoms of life and is known to perform a number of biosynthetic and degradative functions. By analysing plant catalase protein sequences using bioinformatics, it is possible to molecularly clone critical genes and anticipate gene regulatory networks and whole-cell dynamics. Ramachandran plot showed that most of the amino acid residues are in the core region which represent the favourable comformation of amino acid residues of the catalase. In silico study of protein sequences elucidates the various catalytic sites, allowing for potential modification to achieve desired properties.

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Antioxidant defence system during exponential and stationary growth phases of Phycomyces blakesleeanus: Response to oxidative stress by hydrogen peroxide

et al. 2013

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Homology modeling and phylogenetic relationships of catalases of an opportunistic pathogen Rhizopus oryzae

Cited by 3 publications

References 49 publications

Plant catalase in silico characterization and phylogenetic analysis with structural modeling

Plant catalase in silico characterization and phylogenetic analysis with structural modeling

In Silico Studies on Catalases From Plant Sources

Antioxidant defence system during exponential and stationary growth phases of Phycomyces blakesleeanus: Response to oxidative stress by hydrogen peroxide

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